Pregnancy-associated malaria (PAM) is associated with poor pregnancy outcomes. Hemoglobin S (HbS) and hemoglobin C (HbC) mutations are frequently encountered in malaria-endemic areas of Africa, where they protect children from severe and uncomplicated Plasmodium falciparum malaria. However, scant epidemiological data exist on the impact of these Hb variants on PAM. A prospective cohort of 635 Beninese pregnant women was recruited before 24 weeks of gestational age and followed until the end of pregnancy. HbAA, HbAC, and HbAS genotypes were determined and tested for association with pregnancy outcomes and PAM indicators using linear and logistic multivariate models. Newborns from HbAC mothers had higher birthweights than those from HbAA mothers among women infected at any time during pregnancy (mean difference 182.9 g, p = 0.08), or during the first half of pregnancy (654.3 g, p = 0.0006). No such birthweight differences were observed between newborns from HbAS and HbAA mothers. HbAC and HbAS were not associated with other pregnancy outcomes or PAM indicators. In conclusion, HbAC but not HbAS is associated with an improved birth outcome in pregnant women with documented PAM. Higher-birthweight newborns from HbAC mothers may have a survival advantage that contributes to the natural selection of HbC in malaria-endemic areas.